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java.lang.Objectuk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools
uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.CDnaSpliceSiteAnalysisTools
public class CDnaSpliceSiteAnalysisTools
class which contains computing tools for CDnaSpliceSiteAnalysis.
Constructor Summary | |
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CDnaSpliceSiteAnalysisTools()
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Method Summary | |
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private static double |
calcCDnaSpliceSiteGmScore(MyTreeMap minPosTree,
MyTreeMap maxPosTree,
java.util.ArrayList featureArr)
method which calculates the score of a gm. |
private static RecordGmCDna |
checkFeatPosInTree(int featPos,
int maxDistance,
MyTreeMap posTree)
method which checks whether position is in tree or not. |
private static boolean |
doesBoundaryOverlapCDnaIntron(int gmBound,
java.util.ArrayList featureArr)
method which checks if genemodel boundary is overlapping a cDNA intron. |
private static boolean |
doesPosOverlapSimFeatures(int pos,
int fuzzyCDnaBoundaries,
java.util.ArrayList featureArr)
method which returns true if given position overlaps a object in SimFeature ArrayList. |
private static double |
getCDnaScoredSpliceSiteForGm(int debug,
int fuzzyCDnaBoundaries,
GeneModel gm,
java.util.ArrayList featureArr)
methode which calculates the score for one gm (either intron boundaries or splice sites). |
private static java.util.HashMap |
getCDnaScoredSpliceSiteHash(int debug,
int fuzzyCDnaBoundaries,
java.util.HashMap hashCDnaOverlappedGms)
method which gets scored splice sites of genemodels using cDNA evidence. |
static java.util.HashMap |
getCDnaSpliceSiteScoredGmHash(int debug,
int fuzzyCDnaBoundaries,
boolean considerStrand,
java.util.ArrayList _arrListOfGMRegions,
java.util.ArrayList _arrListOfCDnaRegions)
method which returns HashMap of genemodels pointing to their score using a cDNA splice site scoring system. |
private static MyTreeMap |
getGmSpliceSiteTree(int debug,
int fuzzyCDnaBoundaries,
boolean isMinPosTree,
GeneModel gm,
java.util.ArrayList featureArr)
method which creates a tree of either max or min splice sites of the genemodel and overlapping features. |
private static int |
getPositionForPosTree(boolean isMinPosTree,
FeatureComponentAble exon)
method which returns position of exon boundary for position tree. |
private static double |
getTreeScore(MyTreeMap tree,
java.util.ArrayList featureArr)
method which calculates the score of a tree. |
private static MyTreeMap |
putFeatPosInGmTree(MyTreeMap positionTree,
int fuzzyCDnaBoundaries,
boolean isMinPosTree,
java.util.ArrayList featureCompArr)
method which adds SimFeature boundaries to gm boundary tree. |
private static MyTreeMap |
putGmInPosTree(boolean isMinPosTree,
int fuzzyCDnaBoundaries,
java.util.ArrayList gmFeatCompArr,
java.util.ArrayList featureArr)
method which returns a tree of featureComponent positions (Intron, Exon). |
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.tools.BasicFeatureAnalysisTools |
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getGmHashOfOverlappedFeat, isFeatureOverlappingGm |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CDnaSpliceSiteAnalysisTools()
Method Detail |
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public static java.util.HashMap getCDnaSpliceSiteScoredGmHash(int debug, int fuzzyCDnaBoundaries, boolean considerStrand, java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions)
debug
- debugging modefuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice siteconsiderStrand
- switch for strand consideration_arrListOfGMRegions
- ArrayList of genemodel regions_arrListOfCDnaRegions
- ArrayList of cDNA regions
private static java.util.HashMap getCDnaScoredSpliceSiteHash(int debug, int fuzzyCDnaBoundaries, java.util.HashMap hashCDnaOverlappedGms)
debug
- debugging modefuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice sitehashCDnaOverlappedGms
- HashMap of genemodels pointing to
ArrayList of overlapping cDNAs
private static double getCDnaScoredSpliceSiteForGm(int debug, int fuzzyCDnaBoundaries, GeneModel gm, java.util.ArrayList featureArr)
debug
- debugging modefuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice sitegm
- genemodelfeatureArr
- ArrayList of overlapping SimFeature objects
private static MyTreeMap getGmSpliceSiteTree(int debug, int fuzzyCDnaBoundaries, boolean isMinPosTree, GeneModel gm, java.util.ArrayList featureArr)
debug
- debugging modefuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice siteisMinPosTree
- switch for consideration of either start or end
position of the featuregm
- genemodelfeatureArr
- ArrayList of overlapping SimFeature objects
private static MyTreeMap putGmInPosTree(boolean isMinPosTree, int fuzzyCDnaBoundaries, java.util.ArrayList gmFeatCompArr, java.util.ArrayList featureArr)
isMinPosTree
- switch for consideration of either start or end
position of the featurefuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice sitegmFeatCompArr
- ArrayList of genemodel components (genemodel
component positions)featureArr
- ArrayList of overlapping features
private static boolean doesPosOverlapSimFeatures(int pos, int fuzzyCDnaBoundaries, java.util.ArrayList featureArr)
pos
- position of a genemodel (either start or end position)fuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice sitefeatureArr
- ArrayList of overlapping SimFeature objects
private static int getPositionForPosTree(boolean isMinPosTree, FeatureComponentAble exon)
isMinPosTree
- switch for consideration of either start or end
position of the featureexon
- Exon object
private static MyTreeMap putFeatPosInGmTree(MyTreeMap positionTree, int fuzzyCDnaBoundaries, boolean isMinPosTree, java.util.ArrayList featureCompArr)
positionTree
- tree containing RecordGmCDna objectsfuzzyCDnaBoundaries
- contains allowed difference of cDNA and
genemodel splice siteisMinPosTree
- switch for consideration of either start or end
position of the featurefeatureCompArr
- ArrayList of genemodel components
private static RecordGmCDna checkFeatPosInTree(int featPos, int maxDistance, MyTreeMap posTree)
featPos
- position of a genemodel (either start or end position)maxDistance
- contains allowed difference of cDNA and
genemodel splice siteposTree
- position tree containing all splice sites of
genemodel and overlapping SimFeature objects (either start or end
position)
private static double calcCDnaSpliceSiteGmScore(MyTreeMap minPosTree, MyTreeMap maxPosTree, java.util.ArrayList featureArr)
minPosTree
- tree containing RecordGmCDna objects (only start
positions)maxPosTree
- tree containing RecordGmCDna objects (only end
positions)featureArr
- ArrayList of genemodel overlapping features
private static double getTreeScore(MyTreeMap tree, java.util.ArrayList featureArr)
tree
- tree containing RecordGmCDna objectsfeatureArr
- ArrayList of genemodel overlapping features
private static boolean doesBoundaryOverlapCDnaIntron(int gmBound, java.util.ArrayList featureArr)
gmBound
- boundary of a genemodelfeatureArr
- ArrayList of overlapping cDNA features
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